OS X is a real warhorse but, in uncommon circumstances, you might experience boot errors or major system issues.
You might also want to start from scratch because you're unhappy about the overall performance, or you're upgrading to a new version.
There are different schools of thought when it comes down to upgrading. Some think installing the new version on top of the previous one is the way to go, while other think it's best to perform a fresh reinstall.
In all the above cases, you need to use OS X Utilities.